10 commits

Author	SHA1	Message	Date
Yuk Kei Wan	16e8d21477	Nanoplot and sequencing_summary.txt for Nanopore test data (#364) ... * add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output	2021-04-09 08:31:38 +01:00
Anthony Underwood	63b3975292	Update gubbins module to use new files (#417) ... * new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new snpsites module * new snpsites module * new snpsites module * new snpsites module * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * use sars-cov-2 alignment * remove old test alignment * new snpsites module * new snpsites module * new snpsites module * updated test file names * new snpsites module * remove snpsites from gubbins branch * remove redundant test_fas alignment * update md5 sums Co-authored-by: avantonder <avt@sanger.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: avantonder <ajv37@cam.ac.uk>	2021-04-09 07:54:11 +01:00
Jose Espinosa-Carrasco	f90dde0d88	Add plasmidid module (#410) ... * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml	2021-04-08 22:44:30 +01:00
Anthony Underwood	be390a25e5	adding fasttree module (#412) ... * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * remove TODO * update test data naming * further test data naming updates * remove options in favour of $options.args * ensure non standard exit codes don't cause an issue * update md5sum	2021-04-08 18:15:23 +01:00
avantonder	710ab76b90	new module: gubbins (#377) ... * new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-04-07 16:31:24 +01:00
Robert A. Petit III	c9256616b9	update tests for new config (#384) ... * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-04-01 20:22:06 +01:00
Ravneet Bhuller	c5c59d44a1	PR for sequenzautils/bam2seqz (#395) ... * added files * edited files * removed file * README.md edited Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>	2021-04-01 07:08:27 +02:00
Nicholas Toda	e526eae472	Add tests for hisat2 (#366) ... * initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-03-25 21:08:46 +00:00
Jose Espinosa-Carrasco	17fbdf96cb	Fix some module tests after switching to config data (#386) ... * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module	2021-03-24 18:28:07 +00:00
Harshil Patel	83a500e6b0	Use a config containing all test data for module tests (#365) ... * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint * Initial commit for test data config * Rename test data * Include test config * Update indents * Update test for FastQC via config * Remove quotes of bottom-level variables * Use underscores in key names * Get tests working for fastp * Remove whitespace at beginning of file	2021-03-24 13:07:37 +00:00